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epiverse-trace / superspreading

Estimation of individual level variation in transmission
https://epiverse-trace.github.io/superspreading/
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New formula for proportion transmission #99

Closed dcadam closed 2 months ago

dcadam commented 2 months ago

New formula for proportion of transmission which addresses issue #93

joshwlambert commented 2 months ago

@dcadam thanks for making this contribution! I've integrated your new function, proportion_transmission2() into proportion_transmission() and added a method argument that allows users to switch between the "p_80" (original) method and the "t_20" (newly contributed) method. I've integrated the documentation you've provided into the existing proportion_transmission() documentation, this can be viewed with ?proportion_transmission().

The new functionality benefits from all of the existing input checking that proportion_transmission() already had.

I've also added unit tests to make sure the new functionality is working as expected.

As this PR is a great enhancement to the package, I've added you as a package author. Please let me know that you're okay with this before I merge the PR.

Once this PR is merged, I'll try and write a vignette that explores the difference between the two proportion_transmission() methods ($p{80}$ and $t{20}$) to make clear to users of the package when to use each and some of the background theory to both approaches. It would be great if you'd review this vignette once I've drafted something.

dcadam commented 2 months ago

@joshwlambert Thanks for including me. Happy to listed as a package author for this, and to help review the vignette when needed.